[Kalcor]

This is most likely not a result of SA-MP, but of the downgrade patch. The save files will still be there, although version 2.0 save files are incompatible with the 1.0 exe. If you want the saves back just reinstall the game from DVD and you'll have version 2.0 again - but you won't be able to play SA-MP.

Having 2 different GTA SA install folders is one way of getting around it.